Optimum reproduction performance of small ruminants managed under extensive production system can be influenced by the availability of nutrients, especially the mineral content of forages and reproductive management. The present study was conducted to evaluate the effect of Se supplementation and oestrous synchronisation protocols on the reproductive performance of South African indigenous goats during the autumn breeding season. Does (n = 48) were randomly allocated to six treatment groups in a 2x3 factorial design. The factors in the study were Se supplementation (Se supplemented and non-supplemented) and oestrous synchronisation protocols; (progesterone (P4) + male effect, P4 + equine chronic gonadotrophin (eCG) and male effect). The Se supplemented group was dosed with 0.34 mg Se per kg body weight in the form of sodium selenite at 10-days interval. For oestrous synchronisation protocols, all does in the P4 groups were treated with controlled internal drug release (CIDR) for 11 days. At CIDR removal, does in the P4 + eCG group, were intramuscularly injected with 300 IU eCG. While does in the P4 + male effect group, were introduced to a teaser buck wearing an apron. Does in the male effect group did not receive CIDR devices, instead oestrous was naturally synchronised with the aid of teaser buck wearing apron. Reproductive measures taken included, the number of follicles and size of the largest follicle, oestrous response, oestrous onset and duration, gestation length, kidding weight, litter size and pregnancy rate. The results revealed that Se supplementation had no significant effect on the number of follicles, size of the largest follicle, oestrous onset and duration, pregnancy rate, oestrous response, kidding weight, litter size and gestation length. There was no significant difference between oestrous synchronisation treatment groups for their effect on the number of follicles, size of the largest follicle, oestrous response and duration, pregnancy rate, kidding weight and litter size. However, there was significant difference (P < 0.05) between the different oestrous synchronisation protocols on the onset of oestrous. The P4 + male effect protocol had resulted in an earlier onset of oestrous compared to P4 + eCG and male effect groups. The interaction between Se and oestrous synchronisation was significant in terms of kidding weight and oestrous response. It was concluded that Se had no significant influence on the reproductive performance of South African indigenous goats while the addition of the male effect following P4 treatment improved the reproductive performance of South African indigenous goats. Further studies need to be conducted on the use Se supplementation and the addition of the male effect as a reproductive management technique in South Africa indigenous goats.